Regarding Over Representation analysis over identification of DGE genes, firstly I have a set of 1550 genes resulting of RNA Seq. Given this number decided to do ORA instead of GSEA.
After choosing ORA, I have to pass to enrichGO a filtered list according to the fold change:
genes <- names(gene_list[abs(gene_list)> 2]) go_enrich <- enrichGO(gene = genes, universe = gene_list, OrgDb = org.Hs.eg.db, keyType="SYMBOL", ont = "ALL", pAdjustMethod = "fdr", pvalueCutoff = 0.01, qvalueCutoff = 0.05, readable = TRUE)
In this situation the threshold is > 2 however some researchers use value of 1. What is the optimal solution for accurate results? What are the best practices for deciding this number?